Error in setgenoTest_bgenDosage_v2(bgenFile, bgenFileIndex, ranges_to_exclude = ranges_to_exclude

[Qiaolan]

Hi Wei,

Thanks for your time.

I got the error message below when I do saige-gene analysis:

Error in setgenoTest_bgenDosage_v2(bgenFile, bgenFileIndex, ranges_to_exclude = ranges_to_exclude

An interesting thing is that if I use first 100 snps in the group file, there would be no error. In total, I have about 18000 snps in the group file.

My code is below:

Rscript /fs/ess/PAS1501/gaolab/software/saige/SAIGE/extdata/step2_SPAtests.R \ --bgenFile=/fs/ess/PAS1501/gaolab/qldeng/Eden/saige/chr${N}/${x}/saigechr${N}${x}.bgen \ --bgenFileIndex=/fs/ess/PAS1501/gaolab/qldeng/Eden/saige/chr${N}/${x}/saigechr${N}${x}.bgen.bgi \ --sampleFile=/fs/ess/PAS1501/gaolab/qldeng/Eden/saige/chr${N}/${x}/sample_ID.txt \ --GMMATmodelFile=/fs/ess/PAS1501/gaolab/qldeng/Eden/saige_genechr19/chr${N}/${x}/chr${N}${x}_nullmodel.rda \ --varianceRatioFile=/fs/ess/PAS1501/gaolab/qldeng/Eden/saige_genechr19/chr${N}/${x}/chr${N}${x}_varianceRatio.txt.varianceRatio.txt \ --SAIGEOutputFile=/fs/ess/PAS1501/gaolab/qldeng/Eden/saige_gene_chr19/chr${N}/${x}/output_saigechr${N}${x}.txt \ --numLinesOutput=1 \ --groupFile=/fs/ess/PAS1501/gaolab/qldeng/Eden/saige_gene_chr19/chr${N}/${x}/tab_group_splicing_exonicchr${N}${x}.txt \ --sparseSigmaFile=/fs/ess/PAS1501/gaolab/qldeng/Eden/saige_genechr19/chr${N}/${x}/chr${N}${x}_varianceRatio.sparseSigma.mtx \ --IsOutputAFinCaseCtrl=TRUE

Thank you!

Qiaolan

[Ojami]

Just a thought. As I ran into a similar problem, it maybe because of duplicate variants in your BGEN (if you use idstoIncludeFile flag). Otherwise, if you use rangestoIncludeFile flag, the maximum range you can set it 9999.

Hope it helps! /Oveis

[weizhouUMICH]

Thanks @Ojami ! @Qiaolan That's also my guess. Could you please try to see if there are any duplicated variant IDs among the 1800 variants in the variant set?

Thanks, Wei

[Qiaolan]

Thank you, @Ojami and @weizhouUMICH ! I will have have a try today and keep you updated.

[Qiaolan]

I sill had the same error message after I removed duplicated snps in my bgen file.

For example, for gene PSG1:

geneID: PSG1
[1] "PSG1 \t19:43375918\t19:43375918" genetic variants with 0.0002944641 <= MAF <= 0.5 are included for gene-based tests [1] "ids_to_include" [1] "19:43375918" "19:43375918" TEST 2 TEST 1 OK TEST2 2 ranges_to_include.nrow() 0 ranges_to_exclude.nrow() 0 ids_to_include.size() 2 ids_to_exclude.size() 0 Error in setgenoTest_bgenDosage_v2(bgenFile, bgenFileIndex, ranges_to_exclude = ranges_to_exclude, : db::StatementStepError Calls: SPAGMMATtest -> getGenoOfGene_bgen -> setgenoTest_bgenDosage_v2 Execution halted

Initially, 19:43375918 had duplicates in the bgen file. After I removed duplicates, I still got the error above.

Thanks for your help! @weizhouUMICH @Ojami

[Qiaolan]

Problem has been solved. I also need to modify my group file. Thank you anyway!